Here we report a case of Hirschsprung's disease presenting with acute complete splenic infarction due to thrombus in the splenic vena. MTHFR C677T (methylenetetrahydrofolate) gene homozygote mutation was a risk factor for thrombosis. According to our knowledge, this is the first report for a Hirschsprung's disease patient with acute complete splenic infarct due to isolated splenic vein thrombosis accompanied by MTHFR C677T gene homozygote mutation.